Stargate Atlantis: Anomaly
by Neo Queen Saranity
Summary: Alternate realities, clones, replicators and food cravings. Just another day in the Pegasus Galaxy.
1. Chapter 1

**Disclaimer: See Profile for Umbrella Disclaimer. It basically states I own nothing. **

Part 1

Richard Woolsey, current leader of Atlantis, was having a very nice day. He'd just received his glowing review from the IOA and was now considered the permanent leader, for the foreseeable future, of thee Atlantis base. Ever since Atlantis had been re-relocated to the Pegasus Galaxy after its brief ten-month tenure on Earth, his continued leadership had been in question. Now, finally, it was a settle matter again. After many talks, most of which revolved around military control of the base and leaving in on Earth, it was decided that having Atlantis on Earth was just too much of a security risk, weather you sunk it deep in the ocean or attempted to hid it in the most barren portions of a desert. There were just too many organizations that would do anything to get their hands on the Ancient tech Atlantis had to offer, now that a Galaxy wouldn't be standing in their way. This was, incidentally, why it was decided that Atlantis was to go back to Pegasus, among other reasons. This would mean that the only way to dial, and therefore get, to Atlantis, would remain squarely with the SGC, a ZPM. So, all in all, Woolsey was quite happy with the way things were going. He loved leading the Atlantis base. He loved and respected the people hear and would have been quite disappointed to go back to his old life with the IOA. It had been a long three months, locating a new planet, integrating the new and old personnel, and reestablishing trade agreements with old friends, but it had all been worth it. A plus note being they hadn't had any major, and very few minor problems since here return.

"Mr. Woolsey," Woolsey heard from his head piece. "You're needed in the gate room." Here we go, he thought. He looked at his watch, 5:46am Atlantis Standard Time (AST). Here's to hoping our luck holds.

******

"Sir," Cormack said, "we're receiving a data burst."

"IDC?" Woolsey asked?

"No sir"

"Very well, make sure the data is transferred to a non-networked firewalled computer. And why isn't the gate shield up?"

"That's the problem sir, we can't put it up. There seems to be some sort of interference preventing it from operating. The gates been open for the last five minutes while we've been receiving the burst, we've been trying to put it up since. We've called for Dr. McKay and he should be here any second." No sooner had Cormack finished saying this then Dr. McKay came around the corner.

"Just so you know, I was having quite a nice dream before your incompetence and inability to solve simple problems interrupted me. Couldn't Zelenka have handled this?" McKay asked tersely.

"Sir, we can't seem to…"

"Yes, yes I know, move." McKay snapped. He was not a morning person and really had been interrupted from quite a nice dream. But, on the other hand, the thought to himself, he was arguably one of thee (if not thee) smartest people in this galaxy and so it was rather reasonable for him to be called upon to solve the tough problems. Such was the price of greatness.

McKay sat at the terminal and got to work. Forty-five seconds in however, he knew there was trouble.

"Well," asked Woolsey, "what's the problem?"

"First of all, what Einstein over there so cleverly diagnosed as interference is actually a highly complex program designed to nullify the frequency at which the gate shied runs. Very similar to how the program I designed to nullify the gate in order to retake Atlantis from the Replicators works. It will take me a few minutes to recalibrate the shield to negate the frequency, but I have a feeling, whoever is behind this will have finished doing whatever it is there up to long before in can finish." McKay went back the pounding away on the keys. Trying to make sense of what was happening. "No, no, no, no, no. This is not good. Why didn't anyone feel it prudent to mention the anomalous energy readings we received at the beginning of the transmission, didn't anyone else feel that was signif…wait, hold on, we have an incoming traveler."

"Incoming traveler," Cormack yelled down the now tense soldiers guarding the gate.

Moments later, a woman, glowing green, stumbled through the gate, "I made it" she sighed and then the shield flickered and collapsed.

The guards around the gate approached cautiously, Sheppard at the lead. He stared down at the women and then started, with something akin to shock and recognition.

"Carter?" He gasped.

**AN: I really do enjoy reviews and it motivates me to write more but I will attempt to keep up with this story regardless. I hope everyone likes it and don't worry, you won't have to deal with many authors notes from me. Thanks for reading my story.**


	2. Chapter 2

Part 2

Coronel John Sheppard couldn't help thinking that things had been a lot simpler before he'd know about aliens, space travel, and alternate realities; especially those. Well, perhaps he was overstating things. His life before had just been a lot less confusing, though not quite as interesting. He thought there were a few things he could have lived without experiencing though. Being turned into a bug, living six months with Ancient wannabes', being cloned, going to the future and back again, and having an alien entity use his likeness to terrorize his friends' dreams chiefly among them. Never a dull moment in the Pegasus Galaxy that was for sure. He also acknowledged that, while all the craziness was well, crazy. He wouldn't ever trade it in or take back his decision to join the mission given a chance. The people here had become like his family, a much truer family than he had know on earth, and he would die for any of them.

John's biggest concern for the day rested with the recent appearance of one Dr. Samantha Carter. At first he'd just assumed something had gone wrong with a trip from the Milky Way. The intergalactic gate bridge had finally been recommissioned but because of the new necessary security, the systems were still being tested and a little buggy. McKay insisted on blaming Zelenka for that. However, it hadn't been Carter, or more specifically, their Carter. This Samantha Carter was claiming to be from an alternate reality. Their Sam Carter would be coming in a few days to help clear things up, as she'd dealt with this type of situation a few times before, and debrief the….other Carter. John rubbed his head. He just knew that this was going to get confusing, very quickly. He'd been quite happy when alt-Sam had asked him to just call her Dr. Carter in order to dissuade confusion. His Carter would continue to be referred to as Coronel Carter. He rubbed his head again. Youp, this was going to be a long week, tons of paperwork. Great.


	3. Chapter 3

Part 3

Dr. Jennifer Keller glanced at her newest patient for the third time in as many minutes. She wasn't quite sure what to make of this. She'd seen some weird things in the Pegasus galaxy, but this seemed different somehow. Perhaps it was because she considered herself to be quite good friends with Samantha Carter, well, their Carter anyway. She did, in fact, keep regular contact with Sam, even though she was no longer the leader of the Atlantis base. They still wrote to each other regularly and spoke in person whenever possible. Sam was actually getting married in a few months and had asked her, along with Tayla and Vala, to be a bridesmaid. She was quite looking forward to it. It was just so strange to look at this woman, who was, in every since of the word Samantha Carter, but at the same time, completely not.

Dr. Carter, had been very quite since she'd been brought into the medical ward about three hours previously. She'd allowed Keller to run all of test without complaint and had been mostly compliant under questioning. She'd stated, quite adamantly, from the beginning, that she wanted to be debriefed properly, so she wasn't forced to go through this several times over. And really Keller could see her point. Who would want to have to answer the same question over and over and over again to every Tom, Dick and IOA member?

She stole another glance at Dr. Carter. Only this time she'd been caught. She looked away quickly. Now she felt terrible for gawking. Carter wasn't an animal at a zoo or a research project. She was a woman who'd just been through God knew what and didn't need to be stared at. What made her feel worse was the look in Carter's eyes when she'd been caught staring. It hadn't been mad, or accusing, things she was well within her rights to feel, it had been resigned, and Keller realized that this had been no less than what she'd expected. Just great Jennifer, she told herself, alienate the poor woman farther.

As far as Keller could tell, everything Carter had told them, she'd been completely honest about. And according to all of Keller's tests, she was indeed Samantha Carter. Dr. Carter had been fairly tight-lipped about everything other then the strictly necessary. She'd only told us what she believed we needed to know before the debriefing; her name Dr. Samantha Carter, that the green light they'd seen when she'd come through the gate had been an augmented personal shield, designed to only deactivate in the presence of humans with the gene and that the world she had come from, she was unable to return to. And that was it. She had pretty much shut down to any line of personal questioning after that point, and eventually everyone had just left it alone. They'd get their answers soon enough. The last person to leave her side had been Rodney McKay. He'd been extremely interested in her personal shield and was the only person not asking her overtly personal questions. This was probably the reason, several minutes later; Carter had given McKay an indulgent smile and handing over the shield, telling him to "have at it." McKay had skipped off not long after, all eager excitement over his new project. And now Carter sat, or lay, alone in the medical ward with no one to talk to and nothing to do. Keller felt terrible.

She had just decided that she was going to gather all of her courage and have a conversation with her when another thought struck her. It was the main reason, aside from the obvious, for her earlier staring. Well, one of the reasons. She knew something about this Carter that no one else on the base, save for Carter herself, knew. Samantha had asked to speak to her privately. No doubt assuming it would show up eventually anyhow and hoping it could just be between them for now. More out of necessity than actual want, Carter had shared something with Keller. Something that may, or may not, come up in the debriefing. Dr. Samantha Carter was four months pregnant.


	4. Chapter 4

Part 4

After many discussions on how this would go both Carters decided it would be best if they allowed Dr. Carter to tell her story completely before allowing anyone to question her. Coronel Carter smiled a little at how difficult that would be for some of the members of her old team sitting around her.

"I think," said Dr. Carter, "That way to start my story is this." She paused and took a breath. "In my reality, we did not win the war against the replicators. It's, in fact, going quite strong, and it is they who are winning." This declaration was met by shocked faces and people already looking like they wanted to interrupt, McKay and Sheppard chiefly among them. They held their tongues however, when she started speaking again, leaving no room for them to interrupt. "About two years ago the replicators of the Milky Way and Pegasus galaxies' joined forces. The effect upon both galaxies was disastrous and swift. No planet or race was spared. Many of the great races of the Milky Way were destroyed in months. The Jaffa nation is no more, many if not most, of the Asgard are dead, the Nox were completely decimated in the first wave, and many others. In the Pegasus Galaxy the replicators first dealt with their biggest threats the Asgard of that galaxy, the Travelers, and many larger, more technologically advanced cultures or those using ancient technologies. They hit all of the technologically advanced or populace societies first in the hope to cripple our ability to fight back, and it worked.

Atlantis was saved for a while because we were in possession of two ZPMs and it was able to fly. We kept to space mostly in the hopes of not being found. Earth was saved by the use of Merlin's out-of-faze technology. But that didn't last forever. With only one ZPM on earth, the technology could be sustained for a while but not indefinitely. And Earth had no means by which to procure more. Atlantis had been out of contact for over two months while in interstellar hiding. It was decided pretty quickly that with the scale and brutality of this assault that we could not make a stand. We used the only options left to us and build ships with the hope of escaping to where the replicators couldn't, at least for some time, follow.

It was decided that we would try to take as many as we could on a mass relocation. We were leaving the Milky Way and Pegasus galaxies. We couldn't go to the Asgard galaxy as the replicators knew if it. So we went with the only option available to us; The Ori galaxy. We'd recently defeated the Ori and so were not worried about their feeling on this incursion, and they had kept their worshipers so anti technology that we were sure we wouldn't have to worry about any of our ships being attached for a long time. We would find a new planet, preferably uninhabited, and try to start again and maybe one day in the future we would have the technology required to take on the replicators and reclaim or galaxy." She paused again. Not meeting anyone's eyes.

"Most were able to make it, at a price. Our last ship, a modified Goa'uld cargo ship, the least populace of the ships, was in charge of insuring the other ships got through and then setting a device to destroy the Super Gate before going ourselves. The replicators got to us first though and we were forced to destroy the gate before we could make it though. We suffered ship damage in the ensuing fight but were able to jump to hyperspace and escape."

"My husband, (Most of the people in the meeting, including Coronel Carter, glanced at the ring she was now twirling around and around on her finger.) myself, two other scientists and three Marines were left on the Tel'tak. We had limited food and resources and now all of our friends were in another galaxy, which we had no means to reach. Two months went by; our numbers dwindled down from seven to three; my husband, myself, and one other. We came up with a plan to use the stargate to travel to an alternate reality. I'd seen it done myself previously while being a part of SG1. The replicators caught up with us thought and it was all my husband could do but insure I survived. He demanded I go through the gate without him. He had already sent through a data burst and insured that the gate would be open on the other end. He knew he wouldn't be able to make it to the gate and so he sent me through and armed the self destruct in the facility we had been occupying, and so here I am." No one spoke for several minutes and Dr. Carter turned from their pitying looks.

"I'm…well, I don't really know what to say that won't come out…that would be enough to convey how sorry I we are for what you've been through. Of course you are more than welcome to stay here on Atlantis." Finished Mr. Woolsey.

"Thank you Richard." Dr. Carter said, finally looking up. "I also wanted to give you the codes you need to decipher the initial data burst you received before my appearance. It contains several research projects that we'd been working on as well as a program that uses the Ancient ascension machine to change my DNA in a subtle way to insure that I won't suffer cascade tremors because of two Carters existing in the same reality."

"I'd wondered about that." Said Coronel Carter. " I had assumed though that it might not affect you as strongly with us being in spate galaxies, but in the long term it would still have some sort of effect."

"Yes, I'm hoping that with us being separated, I won't have to worry about getting the treatment for at least the next five months."

"But if it could help. Why would you wait?" Asked Dr. McKay. "It seems like you would want to do it as soon as possible.

Dr. Carter smirked at him, already amused by the look she knew he would have. "Well, I'm not exactly worried about what would happen to me. I trust my husband's programming skills." She smiled again, as if to an inside joke. And then, "I am however worried about what it would do to my baby."

**AN: Thanks to everyone who is reading this story. I'm trying to update on a regular basis and I should have the next chapter out in a week or less.**


	5. Chapter 5

AN: For any loyal readers of this story looking for an update. Here it is. I had actually not been thinking about this story. I've been doing more fanfic reading the writing these days. But you can thank Sam Carter McKay, my newest fan (blush) for this post. I have now been reminded that people actually may enjoy reading this story. I'll try to do better. Well now on with the chapter.

Part 5

Pregnant! Sam Carter was pregnant by some unknown husband. He was having a hard time wrapping his mind around it. McKay wondered idly whether or not it would be at all acceptable to slake his morbid curiosity and ask Dr. Carter who the father of her child was. She was married and pregnant, it was just mind boggling, and he just couldn't' get over his want to ask. McKay smiled crookedly at a sudden thought. She would probably hit him for asking. Now that there was one Carter that would have no real repercussions for physical abuse on his person he'd have to be more careful. But, he'd always like spirited women. It might be worth it if he found out what he wanted.

McKay had actually not seen much of Samantha in the last few days. Coronel Carter had left fairly quickly after the debriefing. Not wanting to risk Samantha's baby to a cascade tremor, no matter how unlikely. And after imparting all of the information she could on her personal shield and decrypting the files that had come through the gate before her she'd pretty much left him to it. Come to think of it, if he were honest with himself, he would say that Samantha was avoiding him. He'd seen her eat several meals and hold conversation with his other team members, even Ronan, but she would usually make some excuse to leave whenever he showed up.

McKay went back to the research. The modified shield was really quite amazing. It must have taken quite a gifted individual with a lot of knowledge of Ancient tech to MacIver it to work the way they wanted it to. Samantha had assured him that it hadn't been her but had been quite reluctant to tell him who had modified it. That was another think. Whenever Samantha did see fit to grace him with her prescience she was very closed off. She answered direct questioning, but only when it involved something technical, never personal. She seemed to be getting on with the others well enough though so he was left to assume that it had something to do with him.

Making up his mind McKay walked to Dr. Samantha Carter's quarters. He was determined to get answers and would not leave until he was satisfied. After walking back and forth in front of her door indecisively several times he knocked.

"Samantha, Sam…I know you're in there. I just want to talk."

"Come in." came a soft voice. McKay entered and the door slid closed behind him. "What can I do for you McKay?"

"I…well…it's just…" now that McKay was here, and it seemed harder to get his feelings across, and he also had a feeling he might not like what she had to say. He wasn't quite sure whether he should make something up and leave quickly or ask what he'd originally come for.

"McKay", Samantha prompted. "You said you wanted to talk, what do you need?"

"Why are you avoiding me?" McKay blurted. Great, he thought. Now I've been reduced to word vomit. He'd never been eloquent when dealing with people. He knew he came across as quite abrasive at the best of times and had been hoping to ease into this with more grace. Apparently that was now out of the window. He settled for looking at her expectantly. She was grimacing.

"I'm not sure you want to know." Rodney gave her a dubious look. Her gaze pierced him a moment, as if looking for, and then finding something, and then started again. "I'm not avoiding you, per say, I'm avoiding my past, myself, my name." Now Rodney was confused.

"What does your name have to do with avoiding me?" Dr. Carter then gave him that strange knowing smile.

"My name…is Dr. Samantha Carter-McKay." At this pronouncement Dr. McKay promptly fainted.


End file.
